Pope Francis has announced that he will canonize Franciscan Friar Junipero Serra when he visits the United States in late summer. How does that reconcile with a papal decision made 15 years ago when Pope John Paul II apologized for 2,000 years of violence by the Roman Catholic Church against indigenous peoples, Jews, heretics, women and gypsies?

In the case of California’s missions, the coastal Indians paid a high price for their interaction with the church. Serra, who arrived in 1769, created a harsh and unforgiving regimen that would ultimately claim the lives of 62,000 Indians and devastate their civilization, including the extinction of a number of small tribes.

I have spent the past seven years researching life at the missions through historical documents at Santa Barbara Mission Historical Archives, Mexico’s National Archives in Mexico City and numerous university libraries. I have studied images of documents written in Serra’s hand and little-known letters and reports from Serra and other Franciscans, documents from Spanish governors and military leaders, eyewitness accounts from travelers as well as academic research. The truth is painful and not widely understood.

Overcrowding, exposure to European diseases, harsh punishment and a dramatic change in diet quickly began costing Indian lives. Accustomed to a healthy diet of small animals, fish and root vegetables, Indians were often fed cornmeal mixed with water to sustain them as they toiled tending crops and livestock for the missions.

In Serra’s mind the only future for the Mission Indians was to spend their lives under the control of the friars living in the mission compounds, banning them from returning to their native villages and tribal groups. Baptism, Serra maintained, would guarantee their entry into heaven, the only salvation for the neophytes whom friars referred to as their children.

When Spanish Gov. Felipe de Neve complained to Serra that too many Indians were being harshly punished, Serra replied that these were tried-and-true methods previously used by Francisco Solano, a Spanish missionary in Peru. Serra argued there was no reason that he and his friars should not similarly whip the Indians to keep them under control.

Mission Indians also suffered the use of wooden and iron stocks tightly attached to their legs that would tear their skin. Children as young as 10 years old could receive up to 10 lashes for infractions of mission rules.

European visitors to the mission were appalled at the conditions and treatment of the Indians they witnessed. One of them was a distinguished French admiral, Capt. Jean-Francois de Galaup, Comte de la Perouse, who led a major expedition around the Pacific Rim. In 1786, visiting Mission Carmel, he was shocked that even Indian women were not exempt from being whipped.

“Women,” he said, “are never whipped in public, but in an enclosed and somewhat distant place that their cries may not excite a too lively compassion, which might cause the men to revolt.”

On Feb. 2, 1820, Father Mariano Payeras, the last Spanish director of the 21 California missions, wrote to his superior in Mexico City pleading that something be done to stop the high mortality rates within the missions where the bodies of thousands of neophytes were already filling graves. In reality, he wrote, “even the most pious and kindly of us will answer: The missionary priests baptized them, administered the sacraments to them, and buried them.”

Payeras’ letter bluntly condemning the policies is a clear admission by a member of the Franciscan hierarchy of what Serra’s misguided policies wrought.

Serra was never required to keep the Indians enslaved in the missions. His assignment was to educate them and make them subjects loyal to Spain.

After establishing the missions, his goal became to send Indian souls to heaven. Keeping them from sin by forcibly confining them to the missions was, in his twisted mind, the most efficient manner to achieve that goal.

Despite the record of horrendous deaths of indigenous people, the destruction of their culture and the formal apology for this cruelty from the Roman Catholic Church 15 years ago, Pope Francis has chosen to declare Junipero Serra a saint. I would expect this pope, a product of the New World, to be intimately familiar with the historic suffering of Indians throughout this hemisphere. I am astonished by his decision.

Elias Castillo, a former San Jose Mercury News reporter who lives in San Mateo County, is the author of “A Cross of Thorns: The Enslavement of California’s Indians by the Spanish Missions,” which is available online and will be in bookstores in February. See http://www.eliasacastillo.net/ for Bay Area speaking engagements and book signings. He wrote this article for this newspaper.